iGTP: A software package for large-scale gene tree parsimony analysis

Chaudhary, Ruchi; Bansal, Mukul S.; Wehe, André; Fernández-Baca, David; Eulenstein, Oliver

doi:10.1186/1471-2105-11-574

Cited by 91 publications

(67 citation statements)

References 43 publications

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“…A species tree was inferred using gene tree parsimony implemented in the computer program iGTP (43). Individual gene trees estimated using RAxML were used as input files.…”

Section: Methodsmentioning

confidence: 99%

Resolution of ray-finned fish phylogeny and timing of diversification

Near

Eytan

Dornburg

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

832

938

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Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major rayfinned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three longstanding problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes."Actinopterygii | molecular clock | species tree | Teleostei | Percomorpha R ay-finned fishes (Actinopterygii) are one of the most successful radiations in the long evolutionary history of vertebrates, yet despite the rapid progress toward reconstructing the Vertebrate Tree of Life, only 5% of the ray-finned fish phylogeny is resolved with strong support (1). Actinopterygii contains more than 30,000 species (2), with all but 50 being teleosts (3). Compared with other large vertebrate radiations, such as mammals (4) or birds (5), a general consensus on the phylogenetic relationships and timing of diversification among the major actinopterygian and teleost lineages is lacking (3,6,7). This uncertainty about relationships has prevented the development of a comprehensive time-calibrated phylogeny of ray-finned fishes, which is necessary to understand macroevolutionary processes that underlie their diversity.Most working concepts of actinopterygian relationships are based on morphological data (6, 8), and unlike other clades of vertebrates, there has been no comprehensive effort to resolve the phylogeny of actinopterygians and teleosts using molecular data that sample multiple nuclear genes and include taxa that span the major lineages. Despite the long history of using morphological data in the phylogenetics of ray-finned fishes, there are several areas of uncertainty and disagreement...

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“…A species tree was inferred using gene tree parsimony implemented in the computer program iGTP (43). Individual gene trees estimated using RAxML were used as input files.…”

Section: Methodsmentioning

confidence: 99%

Resolution of ray-finned fish phylogeny and timing of diversification

Near

Eytan

Dornburg

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

832

938

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“…Toxin family gene duplication events were inferred by pruning the gene trees to only contain king cobra and Burmese python genes along with a single outgroup sequence. The ensuing gene trees were analyzed using the duplication and loss criterion in iGTP (55) with the following species tree: [outgroup (king cobra, Burmese python)]. For tests of directional selection, we inferred fully resolved maximum likelihood trees from each of the toxin family datasets using the BEST tree-searching algorithm in PHYML (56).…”

Section: Methodsmentioning

confidence: 99%

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

Vonk

Casewell

Henkel

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

429

428

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Significance Snake venoms are toxic protein cocktails used for prey capture. To investigate the evolution of these complex biological weapon systems, we sequenced the genome of a venomous snake, the king cobra, and assessed the composition of venom gland expressed genes, small RNAs, and secreted venom proteins. We show that regulatory components of the venom secretory system may have evolved from a pancreatic origin and that venom toxin genes were co-opted by distinct genomic mechanisms. After co-option, toxin genes important for prey capture have massively expanded by gene duplication and evolved under positive selection, resulting in protein neofunctionalization. This diverse and dramatic venom-related genomic response seemingly occurs in response to a coevolutionary arms race between venomous snakes and their prey.

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“…For comparison, we also reconstructed the species trees using two alternative approaches: iGTP (DL parsimony method) (Chaudhary et al 2010), and duptree (gene tree parsimony method) (Wehe et al 2008). These two approaches differ from ours by their use of a parsimony framework and the fact that the gene trees need to be reconstructed (Robinson and Foulds 1979) distance to the true gene family trees of the trees reconstructed by PHYLDOG under a simpler model of sequence evolution (JC69) than that used in the simulation (HKY85 with rate heterogeneity among sites) and by PhyML under the same simple model and under the correct model of evolution.…”

Section: Reconstructing the Evolutionary History Of Mammalian Genomesmentioning

confidence: 99%

Genome-scale coestimation of species and gene trees

et al. 2012

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Comparisons of gene trees and species trees are key to understanding major processes of genome evolution such as gene duplication and loss. Because current methods to reconstruct phylogenies fail to model the two-way dependency between gene trees and the species tree, they often misrepresent gene and species histories. We present a new probabilistic model to jointly infer rooted species and gene trees for dozens of genomes and thousands of gene families. We use simulations to show that this method accurately infers the species tree and gene trees, is robust to misspecification of the models of sequence and gene family evolution, and provides a precise historic record of gene duplications and losses throughout genome evolution. We simultaneously reconstruct the history of mammalian species and their genes based on 36 completely sequenced genomes, and use the reconstructed gene trees to infer the gene content and organization of ancestral mammalian genomes. We show that our method yields a more accurate picture of ancestral genomes than the trees available in the authoritative database Ensembl.[Supplemental material is available for this article.]The reconstruction of gene phylogenies based on sequences alone is difficult. First, homologous sequences are often hard to align unambiguously (Wong et al. 2008), which leads to incorrect gene trees and erroneous predictions of events of duplications and losses. Second, sequence alignments generally contain insufficient information to accurately model gene evolution and thus understand their history, as suggested by the positive correlation found between sequence length and congruence to the species tree (Galtier 2007). However, knowing the relationships among the species in which these sequences have evolved can improve gene tree inference. Several methods have successfully implemented this idea by combining sequence evolution models with a model of gene evolution that accounts for duplication and loss (DL) (Vilella et al. 2008;Akerborg et al. 2009;Flicek et al. 2010; Kellis 2010, 2012). Provided the species tree is known, these methods yield significantly better gene trees than other molecular phylogenetic methods. However, because reference species trees themselves generally rely on molecular data, they can be also affected by phylogenetic reconstruction uncertainties and unidentified events of gene duplication and loss. This reveals a circular problem: the reconstruction of a species tree requires identifying events of gene family evolution such as DLs, and both the reconstruction of gene trees and the identification of duplications and losses requires a known species tree. The solution to the conundrum is to explicitly consider this two-way dependence and jointly reconstruct the species phylogeny and the histories of all gene families present in their genomes.The coestimation of gene and species trees requires that several gene families be analyzed simultaneously. This represents a significant departure from existing methods (Vilella et al. 2008;Akerborg et al. 200...

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iGTP: A software package for large-scale gene tree parsimony analysis

Cited by 91 publications

References 43 publications

Resolution of ray-finned fish phylogeny and timing of diversification

Resolution of ray-finned fish phylogeny and timing of diversification

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

Genome-scale coestimation of species and gene trees

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